From 2af6067dfa5440d8639328e483c4e7c59167b2a7 Mon Sep 17 00:00:00 2001 From: "Z.-L. Deng" Date: Wed, 5 Jan 2022 15:08:05 +0100 Subject: [PATCH] Update README.md --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1f614c0..2e01002 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ This repository contains the scripts and pipeline that reproduces the results of In this benchmarking study: variants callers `BCFtools` (v1.9), `VarScan` (v2.4.3), `Freebayes` (v1.2.0), `LoFreq` (v2.1.3.1), `CLC Genomics Workbench` (v11.0.1) were evaluated. For the assembly benchmarking, `ABySS` (v2.1.4), `megahit` (v1.1.3) , `IDBA` (v1.1.3), `SPAdes` (v3.12.0), `Ray` (v2.3.1), `Tadpole` (v37.99) were assessed. The haplotype reconstruction program `Savage` (v0.4.0) was also evaluated. + ### Prerequirements To reproduce the output, you need to use `Bioconda`. @@ -65,7 +66,6 @@ threads: 2 # number of cores to use runOnReads: false # Run the whole analyses on reads. Controlled by the `--slow` option ``` - ### Run the benchmarking **All evaluation can be launched with `run_benchmark.py`** @@ -302,3 +302,6 @@ python3 run_benchmark.py vareval -t 10 -c ~/miniconda3/envs \ -r "" \ -o ``` + +### Citation +Deng ZL, Dhingra A, Fritz A, Götting J, Münch PC, Steinbrück L, Schulz T, Ganzenmueller T, McHardy AC. Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses. Briefings in Bioinformatics. 2020:7. https://doi.org/10.1093/bib/bbaa123